160. Enzymes – A Practical Introduction

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160. Enzymes – A Practical Introduction

 

 

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Syllabus

Preface xi
Acknowledgments xiii
Preface to the First Edition xv
1 A Brief History of Enzymology 1
1.1 Enzymes in Antiquity / 2
1.2 Early Enzymology / 3
1.3 The Development of Mechanistic Enzymology / 4
1.4 Studies of Enzyme Structure / 5
1.5 Enzymology Today / 7
1.6 Summary / 8
References and Further Reading / 10
2 Chemical Bonds and Reactions in Biochemistry 11
2.1 Atomic and Molecular Orbitals / 11
2.2 Thermodynamics of Chemical Reactions / 23
2.3 Acid—Base Chemistry / 29
2.4 Noncovalent Interactions in Reversible Binding / 32
2.5 Rates of Chemical Reactions / 35
2.6 Summary / 41
References and Further Reading / 41
3 Structural Components of Enzymes 42
3.1 The Amino Acids / 42
3.2 The Peptide Bond / 53
3.3 Amino Acid Sequence or Primary Structure / 55
3.4 Secondary Structure / 57
3.5 Tertiary Structure / 62

3.6 Subunits and Quaternary Structure / 65
3.7 Cofactors in Enzymes / 68
3.8 Summary / 71
References and Further Reading / 74
4 Protein‒Ligand Binding Equilibria 76
4.1 The Equilibrium Dissociation Constant, K / 76
4.2 The Kinetic Approach to Equilibrium / 78
4.3 Binding Measurements at Equilibrium / 80
4.4 Graphic Analysis of Equilibrium Ligand Binding Data / 88
4.5 Equilibrium Binding with Ligand Depletion (Tight Binding
Interactions) / 94
4.6 Competition Among Ligands for a Common Binding Site / 95
4.7 Experimental Methods for Measuring Ligand Binding / 96
4.8 Summary / 107
References and Further Reading / 108
5 Kinetics of Single-Substrate Enzyme Reactions 109
5.1 The Time Course of Enzymatic Reactions / 109
5.2 Effects of Substrate Concentration on Velocity / 111
5.3 The Rapid Equilibrium Model of Enzyme Kinetics / 113
5.4 The Steady State Model of Enzyme Kinetics / 115
5.5 The Significance of kand K / 120
5.6 Experimental Measurement of kand K / 124

5.7 Other Linear Transformations of Enzyme Kinetic Data / 133
5.8 Measurements at Low Substrate Concentrations / 136
5.9 Deviations from Hyperbolic Kinetics / 137
5.10 Transient State Kinetic Measurements / 141
5.11 Summary / 145
References and Further Reading / 145
6 Chemical Mechanisms in Enzyme Catalysis 146
6.1 Substrate—Active Site Complementarity / 147
6.2 Rate Enhancement Through Transition State Stabilization / 151
6.3 Chemical Mechanisms for Transition State Stabilization / 154
6.4 The Serine Proteases: An Illustrative Example / 178
6.5 Enzymatic Reaction Nomenclature / 184
6.6 Summary / 186
References and Further Reading / 186
7 Experimental Measures of Enzyme Activity 188
7.1 Initial Velocity Measurements / 188
7.2 Detection Methods / 204
7.3 Separation Methods in Enzyme Assays / 223
7.4 Factors Affecting the Velocity of Enzymatic Reactions / 238
7.5 Reporting Enzyme Activity Data / 257
7.6 Enzyme Stability / 258
7.7 Summary / 263
References and Further Reading / 263
8 Reversible Inhibitors 266
8.1 Equilibrium Treatment of Reversible Inhibition / 268
8.2 Modes of Reversible Inhibition / 270
8.3 Graphic Determination of Inhibitor Type / 273
8.4 Dose—Response Curves of Enzyme Inhibition / 282
8.5 Mutually Exclusive Binding of Two Inhibitors / 287
8.6 Structure—Activity Relationships and Inhibitor Design / 291
8.6 Summary / 303
References and Further Reading / 303
9 Tight Binding Inhibitors 305
9.1 Identifying Tight Binding Inhibition / 305
9.2 Distinguishing Inhibitor Type for Tight Binding Inhibitors / 307
9.3 Determining K

for Tight Binding Inhibitors / 310
9.4 Use of Tight Binding Inhibitors to Determine Active Enzyme
Concentration / 313
9.5 Summary / 315
References and Further Reading / 316
10 Time-Dependent Inhibition 318
10.1 Progress Curves for Slow Binding Inhibitors / 321
10.2 Distinguishing Between Slow Binding Schemes / 325
10.3 Distinguishing Between Modes of Inhibitor Interaction with
Enzyme / 330

10.4 Determining Reversibility / 332
10.5 Examples of Slow Binding Enzyme Inhibitors / 334
10.6 Summary / 348
References and Further Reading / 349
11 Enzyme Reactions with Multiple Substrates 350
11.1 Reaction Nomenclature / 350
11.2 Bi Bi Reaction Mechanisms / 352
11.3 Distinguishing Between Random and Compulsory Ordered
Mechanisms by Inhibition Pattern / 357
11.4 Isotope Exchange Studies for Distinguishing Reaction
Mechanisms / 360
11.5 Using the King—Altman Method to Determine Velocity
Equations / 362
11.6 Summary / 364
References and Further Reading / 366
12 Cooperativity in Enzyme Catalysis 367
12.1 Historic Examples of Cooperativity and Allostery in Proteins / 368
12.2 Models of Allosteric Behavior / 373
12.3 Effects of Cooperativity on Velocity Curves / 379
12.4 Sigmoidal Kinetics for Nonallosteric Enzymes / 382
12.5 Summary / 383
References and Further Reading / 384
Appendix I. Suppliers of Reagents and Equipment for

Enzyme Studies 385

Appendix II. Useful Computer Software and Web Sites

for Enzyme Studies 387
Index 391

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